6-124422361-A-G

Variant names:

• chr6-124422361-A-G
• rs531930
• NM_001040214.3:c.273+67014A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040214.3(NKAIN2):​c.273+67014A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 151,888 control chromosomes in the GnomAD database, including 48,599 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.80 (48599 hom., cov: 30)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.865
• Publications: 5 publications found

Genes affected

NKAIN2 (HGNC:16443): (sodium/potassium transporting ATPase interacting 2) This gene encodes a transmembrane protein that interacts with the beta subunit of a sodium/potassium-transporting ATPase. A chromosomal translocation involving this gene is a cause of lymphoma. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040214.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN2	NM_001040214.3	MANE Select	c.273+67014A>G		intron	N/A	NP_001035304.1	Q5VXU1-1
	NKAIN2	NM_001300737.2		c.270+67014A>G		intron	N/A	NP_001287666.1	Q5VXU1-3
	NKAIN2	NM_153355.5		c.273+67014A>G		intron	N/A	NP_699186.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN2	ENST00000368417.6	TSL:5 MANE Select	c.273+67014A>G		intron	N/A	ENSP00000357402.1	Q5VXU1-1
	NKAIN2	ENST00000368416.5	TSL:1	c.273+67014A>G		intron	N/A	ENSP00000357401.1	Q5VXU1-2

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121049 AN: 151770 Hom.: 48552 Cov.: 30

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.686

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.758

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.798 AC: 121158 AN: 151888 Hom.: 48599 Cov.: 30 AF XY: 0.799 AC XY: 59328 AN XY: 74242

African (AFR) AF: 0.866 AC: 35882 AN: 41436

American (AMR) AF: 0.743 AC: 11350 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2451 AN: 3468

East Asian (EAS) AF: 0.870 AC: 4456 AN: 5122

South Asian (SAS) AF: 0.834 AC: 4005 AN: 4804

European-Finnish (FIN) AF: 0.804 AC: 8459 AN: 10520

Middle Eastern (MID) AF: 0.686 AC: 199 AN: 290

European-Non Finnish (NFE) AF: 0.765 AC: 52022 AN: 67968

Other (OTH) AF: 0.757 AC: 1591 AN: 2102

Alfa AF: 0.770 Hom.: 104183

Bravo AF: 0.793

Asia WGS AF: 0.841 AC: 2914 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.63
DANN	Benign	0.48
PhyloP100		-0.86
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs531930; hg19: chr6-124743507;